Molecular Dynamics Workshop Series, March 1-2, 2010

Simbios' Molecular Dynamics Workshop Series consisted of two workshops:

  • Running and Developing Molecular Dynamics (MD) Algorithms on GPUs with OpenMM

    The workshop was intended for those interested in running MD simulations on graphics processing units (GPUs) and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. Some programming background was required. During the workshop, participants learned to:

    • Set up simulations using OpenMM, a freely downloadable library that enables MD simulations to run on high performance computer architectures. It has demonstrated significant speed ups for both implicit solvent[1] and explicit solvent simulations[2] on GPUs.
    • Use OpenMM's custom force options to design and test new MD algorithms
    • Use PyOpenMM, the Python version of OpenMM that is ideal for rapid code development but still achieves high performance
  • Introduction to Molecular Dynamics (MD) and Trajectory Analysis with Markov State Models

    This workshop was intended for researchers (including novices to MD) interested in using MD and/or analyzing MD results in their research. During the workshop, participants:

    • Learned the theory behind MD
    • Used the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs.
    • Learned different techniques for analyzing MD simulations, including Markov State Models and why they are suitable for this
    • Gained hands-on experience with the MSMBuilder software[3] to automatically construct Markov State Models for trajectory analysis

    OpenMM 1.0 and OpenMM Zephyr 1.0 are currently accelerated only on specific NVIDIA GPU cards, but future releases will provide support for ATI GPUs via the OpenCL platform.


         March 1: Running and Developing MD Algorithms on GPUs with OpenMM
         March 2: Introduction to MD and Trajectory Analysis with Markov State Models


    Workshop Logistics

    The workshops were held at Stanford University and were free to attend.

    Additional details (including directions, travel, & lodging info).

    [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872.
    [2]Eastman, P. and Pande, V.S. (2009). Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit. Journal of Computational Chemistry. (In press)
    [3] GR Bowman, X Huang, and VS Pande, "Using generalized ensemble simulations and Markov state models to identify conformational states," Methods, 49(2):197-201.